Interaction between Poly [ADP-ribose] polymerase 1 (4oqa_D) and DNA (26-MER) (4oqa_M_N)

PDB and SCOP data

PDB ID: 4oqa (all binary interactions in this PDB entry)

Title: Structure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.6 Å

  • Chain A: 4oqa_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqa_M_N

    Title: DNA (26-MER)

    Number of residues: 52

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 549.85 Å2

Number of inter-residue contacts at the interface: 40

Number of H-bonds: 5

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 4oqa_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12 E 0.2 1.0 %
    2 15 15 K 51.9 41.1 %
    3 16 16 S 29.8 70.1 %
    4 18 18 R 97.0 51.2 %
    5 19 19 A 35.2 98.4 %
    6 20 20 S 21.7 31.9 %
    7 22 22 K 19.6 19.3 %
    8 34 34 R 18.4 100.0 %
    9 41 41 S 4.5 41.3 %
    10 43 43 M 13.8 7.8 %
    11 44 44 F 70.2 71.1 %
    12 45 45 D 0.8 0.5 %
    13 47 47 K 0.7 0.6 %
    14 48 48 V 33.5 86.0 %
    15 49 49 P 19.1 38.3 %
    16 51 51 W 24.8 74.0 %
    17 259 152 N 14.0 14.6 %
    18 262 155 K 8.8 10.8 %
    19 273 166 P 2.1 16.0 %
    20 274 167 S 39.8 38.4 %
    21 275 168 G 29.5 87.3 %
    22 276 169 E 12.4 13.3 %
    23 277 170 S 1.9 3.8 %

  • Interface residues in 4oqa_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 23 23:M1 A 71.9 38.4 %
    2 24 24:M1 G 112.7 58.8 %
    3 25 25:M1 G 99.3 64.4 %
    4 26 26:M1 C 131.8 48.7 %
    5 27 1:N1 G 73.6 29.7 %
    6 30 4:N1 T 3.4 1.8 %
    7 31 5:N1 A 29.9 15.9 %
    8 32 6:N1 C 13.2 7.4 %
    9 34 8:N1 G 11.9 6.3 %
    10 35 9:N1 G 2.2 1.3 %

No. Residue no. in chain A structure Residue no. in chain A sequence Residue in chain A Residue no. in chain B structure Residue no. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 12 12 E 25 25:M1 G 0.2
2 15 15 K 24 24:M1 G 46.2
3 15 15 K 25 25:M1 G 5.8
4 16 16 S 24 24:M1 G 14.5 H-bond
5 16 16 S 25 25:M1 G 15.2 H-bond
6 18 18 R 23 23:M1 A 4.6
7 18 18 R 24 24:M1 G 24.9
8 18 18 R 25 25:M1 G 21.0
9 18 18 R 30 4:N1 T 3.4
10 18 18 R 31 5:N1 A 29.9
11 18 18 R 32 6:N1 C 13.2
12 19 19 A 25 25:M1 G 24.1
13 19 19 A 26 26:M1 C 11.2
14 20 20 S 26 26:M1 C 21.7 H-bond
15 22 22 K 26 26:M1 C 19.6
16 34 34 R 25 25:M1 G 18.4 H-bond
17 41 41 S 26 26:M1 C 4.4
18 41 41 S 27 1:N1 G 0.2
19 43 43 M 26 26:M1 C 1.7
20 43 43 M 27 1:N1 G 12.2
21 44 44 F 26 26:M1 C 9.8
22 44 44 F 27 1:N1 G 60.4
23 45 45 D 27 1:N1 G 0.8
24 47 47 K 26 26:M1 C 0.7
25 48 48 V 26 26:M1 C 33.5
26 49 49 P 25 25:M1 G 2.3
27 49 49 P 26 26:M1 C 16.8
28 51 51 W 25 25:M1 G 12.3
29 51 51 W 26 26:M1 C 12.5
30 259 152 N 34 8:N1 G 11.9
31 259 152 N 35 9:N1 G 2.2
32 262 155 K 23 23:M1 A 8.8
33 273 166 P 23 23:M1 A 2.1
34 274 167 S 23 23:M1 A 39.7 H-bond
35 274 167 S 24 24:M1 G <0.1
36 275 168 G 23 23:M1 A 16.7
37 275 168 G 24 24:M1 G 12.9
38 276 169 E 23 23:M1 A <0.1
39 276 169 E 24 24:M1 G 12.3
40 277 170 S 24 24:M1 G 1.9

Analyse interface in VoroContacts server

  • Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2

    Result domain: 4oqa_D; Poly [ADP-ribose] polymerase 1

    Alignment data:

    Expectation value = 1.38e-4, Score = 48 bits (112),

    Identities = 32% (26/82), Positive = 54% (44/82), Gaps = 4% (3/82).

    Interface alignment data:

    Interface residues in alignment: 70% (16/23).

    Identities = 31% (5/16), Positive = 56% (9/16), Gaps = 0% (0/16).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

    E +++ + V+YAK G A CKKC E I K R+ +V +P + G + WYH C ++

    4oqa_D: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

    dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEE--HHH--


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqa_D: 61 GHSIRHPDVEVDGFSELR-WDD 81

    dssp: ------HHHHEE------ HHH


    Download alignment FASTA file